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biology 1201 final notes- includes gardiner & waugh.docx

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Western University
Biology 1201A
Michael Gardiner

Lecture 1: - Anthony van Leeuwenkoek made microscopes, first person to see cells and write down results of what he saw - Magnification is an enlargement of what you’re looking at without changing it - Resolution is how close two little dots can be by still looking like two little dots and not merging together - Advent microscope allowed people to look at cells much closer to see viruses - Transmission electron microscope can see inside the cells (cut cells open) but cells must be dead - Scanning Electron Microscope looks at surface of things, cells can be alive - Minimum resolution of light microscope is 0.2 (size of small bacterium) and light microscopes can magnify up to 1000x the size - Cell fractionation is taking cells apart to study their components - Centrifuge: fractionate cells and separate their major organelles (used to figure out interactions, breaks the cell open and sorts through all the components in order to see whats happening) - The cell is the simplest collection of matter which has all the properties of life - Virus can occur in any organism - Some virus can be harmful some have no presence - Can only reproduce when entered into a cell - Two types of cells: prokaryotic and eukaryotic - Prokaryotic have no nucleus (genetic info is in area called nucleoid, no membrane), have a plasma membrane (determines what goes in and out), ribosomes, nucleoid, cytoplasm, cell wall, pili (rodlike structures around the cell), flagella (for movement), mesosomes, photosynthetic membranes - Bacterias range from all sizes and shapes, some are motile and some are not - Eukaryotic cells have a nucleus and are found in protists, fungi, animals and plants - Eukaryotes have plasma membrane, cytoplasm (liquidy part where everything is stored), nucleus, ribosomes, organelles, endomembrane system, cytoskeleton (gives shape to the cell), (cell wall, cell matrix, some organelles, flagella) - Nucleus is usually the largest organelle, most of the genes stores here (some in mitochondria and chloroplasts), about 5 microns in diameter, has a double membrane separating it from cytoplasm but has pores to allow macromolecules and particles to pass - Not everything is allowed in and out of nucleus (ex. Proteins are allowed in) - DNA and associated proteins are organized into chromatin - As cell prepares to divide, chromatin, chromatin turns into chromosomes - In the nucleus there is the nucleolus, where rRNA is synthesized and assembled with proteins with the cytoplasm to form ribosomal subunits - Some organisms have more than 1 nucleus, animals only have one - Cytoplasm is the term for everything in the cell between the nucleus and the plasma membrane, contains all the enzymes the cell will need (approx. 80% water, nucleic acids, proteins, lipds, carbs, pigments, etc) - Ribosomes contain rRNA and protein and has two subunits that carry out protein synthesis - Two endoplasmic reticulums: rough (with ribosomes) and smooth, runs through the cells - Cells that synthesize large quantities of proteins have lots of ribosomes - Free ribosomes are suspended in the cytosol and synthesize proteins that function within the cytosol - Bound ribosomes are attached to the endoplasmic reticulum (can switch between roles) - Many internal membranes in a eukaryotic cells are part of the endomembrane system - Membranes can be in direct contact or connected via transfer of vesicles (sacs of membrane) - Endomembrane system includes: nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vacuoles, plasma membrane - Smooth ER is rich in enzymes and plays a role in a variety of metabolic processes, it synthesizes lipids (including oils, phospholipids and steroids), also catalyzes a key step in the mobilization of glucose from stored glycogen in the liver - Other enzymes in the smooth Er of the liver help detoxify drugs and poisons - Rough ER is especially abundant in those cells that secrete proteins - Secretory proteins are packaged into transport vesicles that carry them to their next stage - Rough ER is also a membrane factory (membrane bound proteins are synthesized directly into the membrane, enzymes in the rough ER also synthesize phospholipids from precursors in the cytosol, as the ER membrane expands, parts can be transferred as transport vesicles to other components of the endomembrane system) Lecture 2: - golgi apparatus transport vesicles from ER, center of manufacturing, warehousing, sorting and shipping - golgi apparatus have cisternae (flat membranous sacs that lok like a sac of pita bread) - cis side receives material by fusing with vesicles, while the other side, the trans side buds off vesicles that travel to other sites (where vesicles leave the gogli) - when the vesicle leaves it can go anywhere therefore there are tags on it telling it where to go - when the vesicle travels from the cis to the trans, products from the ER are modified to reach their final state - can manufacture its own macromolecules, including pectin - tags, sorts and packages materials into transport vesicles - lysosomes are membrane-bounded sacs of hydrolytic enzymes that digest molecules (work best at pH 5) - massive leakage from lysosomes can destroy a cell (autodigestion) - phagocytosis: when something is infused into the cell (lysosomes can then fuse with something brought into the cell) - autophagy is the break down of a material for another use (ex. Tadpole turning into a frog) - vacuoles are larger versions of vesicles (food vacuoles fuse with lysosomes, contractile vacuoles found in freshwater protists, pump excess water out of the cell and central vacuoles are found in many mature plant cells) - plant central vacuoles (biggest part of the cell in a plant), have a membrane surrounding it called the tonoplast, and it transports solutes into the central vacuole - functions: stockpiling proteins or inorganic ions, depositing metabolic byproducts, storing pigments and storing defensive compounds against herbivores - cell wall of a plant gives it shape and strength - tonoplast distinguishes between the central vacuole and other vacuoles - mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work - mitochondria generate ATP in cellular respiration (oxygen produces co2 and atp) - chloroplasts are the site of photosynthesis (light energy to produce sugar) - mitochondria has a double membrane system and the inner membrane increases the surface area, folds in the membrane are called cristae (equivalent to cytosol in the matrix), very rare to get mitochondria from father, usually from mother - inside membranes are thylakoid membranes that have important pigments for photosynthesis - membranes are stacked to get as much light as possible (differs in all plants) - peroxisomes are found in plant and animal cells, they are single membrane bound compartments, enzymes that transfer hydrogen from various substrates to oxygen which produces hydrogen peroxide which is converted to water - cytoskeleton (network fibers extending through the cytoplasm) organizes the structures and activities of the cell Property Microtubules Mifrofilaments Intermediate Filaments Structure Hollow tubules Two Fibrous intertwined proteins super strands coiled Diameter 25nm 7nm 8-12nm Protein Tubulin Actin Keratin proteins Subunits Function Maintain cell Maintain cell Maintain cell shape, cell shape, change shape, organelle motility, cell shape, anchorage chromosome muscle movement, contraction, organelle cytoplasmic movement, streaming, cell track that division proteins can travel on - microtubules grow out of the centrosome (region located near nucleus) - within centrosome of animal cell are a pair of centrioles (9 sets of triplet microtubules arranged in a ring, not in plant cells) - during cell division the centrioles replicate - lots of cilia on cell surface, one or few flagella, cilia gives motility through water - dynein grabs on to the microtubules and then releases them - anchoring junctions: two cells attached by intercellular filaments, rivet cells together - tight junctions: prevent materials from moving between cells, form a belt around cell - gap junctions: intercellular connections between animal cells Lecture 3: - cells need a complete set of genetic instructions, required molecules and direct life processes to survive - cells divide for growth, repair and development - cell cycle: cell grows, adding more cytoplasmic constituents, dna is replicated, cell divides into two identical daughter cells - cell division transmits a complete copy of genetic information and transmits materials necessary for cell to survive and use genetic information - prokaryotic cell division is called binary fission - circular chromosome attaches to one point on the plasma membrane, chromosome is replicated and attached to plasma membrane at a different nearby point, cell elongates and new plasma membrane is added between chromosomes pushing them towards opposite ends of the cell, plasma membrane grows inward at the middle of the cell and parent cell is divided into two identical daughter cells - eukaryotic chromosomes contain almost all the genetic information, humans have 46 strands (46 chromosomes) - DNA + bound protein (protect, package, duplicate, regulate) = chromatin - During non-division phase of cell cycle, cell can only use DNA to produce molecules when in extended state (chromatin) - During division phase of cell cycle, DNA molecules condense to form chromosomes prior to division, each chromosome is a single molecule of DNA, easier to sort and organize DNA into daughter cells (example: chromatin is ike a slinky, cannot move 46 of them around without getting tangled, therefore condense them and they are able to move) - Ploidy: number of pairs of chromosomes in the cell - Haploid: one copy of each chromosome (n) - Diploid: two copies (pair) of each chromosomes (2n) - Polyploid: more than 2 complete sets - 2 major phases in cell cycle: interphase (DNA uncondensed) and mitosis (DNA condensed) - interphase is the longest part of cell cycle (g1, s, g2) - g1 is the first gap where size of the cell increases, organelles may replicate, wouldn’t see any chromosomes (looks normal) - S phase is dna synthesis where dna is replicated, synthesis of proteins associated with DNA, ploidy does not change - G2 is the second gap where the cell prepares for division, synthesis of proteins associated with mitosis cell committed to divide (too much dna for mitosis to not occur) - In phrophase the chromatin fibres become tightly coiled chromosomes, mitotic spindle begins to form - In prometaphase the nuclear envelope fragments, microtubules connect to chromosomes, kinetochores have formed (attaches to the region in the area that the microtubule will connect), some microtubules connect with those from the opposite pole - In metaphase, centrosomes are now at opposite poles, chromosomes at the metaphase plate, centromeres of the chromosomes are on the metaphase plate, kinetochores of each chromatid connected to microtubules from different pole - In anaphase, chromosomes move to opposite poles, move centromere first, poles of cell move further apart - Chromatids attach to microtubules via kinetochores (protein complexes) - Pull the chromatids apart after the centromere breaks apart - In telophase, daughter nuclei form at the two poles, nuclear envelope reforms, chromatin fibres become less condensed, nucleolus reforms, mitosis complete Lecture 4: - cytokinesis is not part of mitosis, it is the process of splitting daughter cells apart (optional) - actin filaments pinch in the cell in animal cells for cytokinesis - timing and rate of cell of division in different parts of a plant or animal are crucial to normal development (skin cells divide regularly, liver cells if needed, nerve and muscle do not) - regulation - at the g1 checkpoint, the cell will receive a go-ahead and will complete cell cycle and divide, if it does not it will exit the cycle and switch into a nondividing state called g0 phase - g0 is when the cells are still living and can still carry out necessary functions, cell cycle is turned off because there is no need for them to divide - important to have controlled growth (ex cancer) - egg and sperm cells are haploid, fuse to make diploid zygote - male gives 23 chromosomes, female gives 23 chromosomes - asexual reproduction is when the individual inherits all its genes from one parent therefore offspring are genetically identical to parent (genetic variation only comes from mutations therefore might cause a problem passing on a mutation, but positive is that you can reproduce quickly) - sexual reproduction each new individual has half genetic info from mom and half from dad therefore offspring are genetically different (more variation) - animals are diploid organism, they produce haploid organism but there are no haploid human beings - fungi are haploid organisms, only become diploid to reproduce - plants can live as a haploid for a while and for a diploid for a while - homologous chromosomes are of the same size, contain the same gene loci (location), may contain different alleles, a diploid nucleus contains two ses of homologs - female- XX, male-XY (sex chromosomes), autosomes are all other non-sex chromosomes - x has 179 known genes, y has 13 - meiosis produces 4 haploid cells, meiosis I and meiosis II, meiosis reduces the ploidy level from 2n to n, meioisis 2 divides the remaining set of chromosomes in a mitosis-like process (differences between mitosis and meiosis occur in meiosis I) - overview of meiosis: mom and dad’s dna replicates, cross over occurs, splits into two, then each cell splits into two again resulting in 4 - in prophase I, the chromosomes condense and homologous chrmosomes pair up to form tetrads - metaphase means lining of the homologous pairs because we are going to pull the pairs apart - in anaphase I, the homologous chromosomes separate and are pulled toward opposite poles - in telophase I, movement of homologous chromosomes contunies until there is a haploid set at each pole then cytokinesis happens - in prophase II, a spindle apparatus forms, attaches to kinetochores of each sister chromatids and moves them around - in metaphase II, the sister chromatids are arranged at the metaphase plate - at anaphase II, the centromeres of sister chromatids separate and the now separate sisters travel toward opposite poles - in telophase II, separated sister chromatids arrive at opposite poles and then cytokinesis happens resulting in four daughter cells - the chromosome number is reduced by half in meiosis but not in mitosis - mitosis produces daughter cells that are genetically identical to the parent and to each other - meiosis produces cells that differ from the parent and each other - 3 unique events to meiosis: synapsis, in metaphase, pairs of chromosomes are aligned not individual, at anaphase, it is homologous chromosomes not sister chromatids that separate - independent assortment means that in any metaphase arrangement, they can line up in different ways (contributes to genetic variability) - number of combinations possible for independent assortment is 2^n where n is the haploid number of the organism - crossing over produces recombinant chromosomes - random fertilization adds to genetic variation (any sperm can fuse with any egg) - 3 sources of genetic variability: independent assortment of homologous chromosomes during meiosis I and of nonidentical sister chromatids during meiosis II, crossing over between homologous chromosomes in prophase I, random fertilization of an ovum by a sperm Lecture 5: - gregor mendel did the pea experiment, peas had 7 traits that gave results Mendel could understand, other traits he could not - 7 traits: round or wrinkled ripe seeds, yellow or green seeds, purple or white petals, green or yellow unripe pods, inflated or pinched ripe pods, axial or terminal flowers and long or short stems - mendels plan was to control fertilization, uses pollen from one plant to fertilize the other - mendel would cross pollinate (hybridize) two contrasting, true-breeding pea varieties (true-breeding parents are the P generation and their hybrid offspring are the F1 generation) - he would then allow the F1 hybrids to self-pollinate to produce an F2 generation - character: a heritable feature, trait: a variant of a character, true breeding: organisms which when they breed produce the same characters, hybridization: mating or crossing two varieties, monohybrid cross: cross that tracks the inheritance of a single character - mendel started with true breeding plants, if you cross yellow with yellow, you get yellow and if you cross green with green, you get green - he then studied a single trait (crossed green with yellow and saw f1 an f2 generations) - phenotype is based on how they look, genotype is based on the alleles - law of segregation: alleles segregate in gametes (no blending), each gamete contains only one allele. The two chromosomes of a homologous pair separate (are segregated) during metaphase I of meiosis I. - dominant alleles mask the expression of recessive alleles in heterozygotes - relates to meiosis because homologous chromosomes may have different alleles for seed colour - not possible to predict genotype from phenotype, but it is possible to predict phenotype from genotype - a test cross is used to determine the identity of the unknown allele (breeding a homozygous recessive with a dominant phenotype) - Law of independent assortment: each pair of alleles segregates into gametes independently (saying that Y does not have to stick with R and y does not have to stick with r). occurs as the various homologous pairs of chromosomes within a cell assort independently during anaphase I of meiosis I. Lecture 6: - Multiplication to determine probability: p(z) x p(y) … etc - Addition rule: “probability that they will be the same is” p1 + p2 - Incomplete dominace is when a cross between organisms with two different phenotypes produces offspring with a third phenotype that is a blending of the parental traits (ex. Red x white = pink) - This is due to the heterozygote having less pigment than the homozygote - Codominance is when both alleles are separately manifest in the phenotype, a single gene locus at which two allelic variations are possible (ex. MM blood group, NN blood groups and MN blood group) - If there are 4 or more possible phenotypes for a particular trait, then more than 2 alleles for that trait must exist in the population (called multiple alleles) - A population can have multiple alleles, but a person can only have 2 alleles - Excellent example: blood type exists for as four possible phenotypes: a, b, ab & o. there are three alleles for the gene that determines blood type. - iA = type a, iB = type b, i = type o because o is recessive, a and b are not - pleiotropy is the ability of a gene to affect an organism in many ways, two affects from one allele (first effect is cat with all white fur, second effect is that cats with all white fur are often deaf in one or both ears) - epistasis is when one gene masks the expression of a different gene for a different trait - quantitative characters: characters vary in the population along a continuum - polygenic inheritance: additive effect of two or more genes on a single phenotypic character - pedigree analysis: information from a family tree or pedigree - symbols on a pedigree: square = male, circle = female, shaded = affected, unshaded = not affected - autosomal recessive pedigree would skip a generation - autosomal dominant pedigree is present in all generations Lecture 7: - Mendelian inheritance has its physical basis in the behavior of chromosomes during sexual life cycles - Around 1900, cytologists and geneticists began to see parallels between the behavior of chromosomes and the behavior of Mendel’s factors - Chromosomes and genes are both present in diploid cells, homologous chromosomes separate and alleles segregate during meiosis, fertilization restores the paired condition for both chromosomes and genes - Thomas Hunt Morgan was the first person to associate a specific gene with a specific chromosome - Experimented on the Drosophila melanogaster, a fruit fly species that eats fungi on fruit - They are small and easily reared in the laboratory, they have a short life cycle (new generation every 2 weeks), a female lays hundreds of eggs during her brief life span (large populations make statistical analysis easy and reliable), giant chromosomes, only have 4 chromosomes, lots of activity going on in the salivary glands, chromosomes replicate but don’t separate, a lot of transcription can occur, little bristles on the leg of the fly to help determine sex - In his study, all the flies were the same but then he eventually came across a fly with white eyes instead of the usual red. The normal character phenotype is the wild type (red) and the alternative traits are mutant phenotypes. Did not know how to create mutations, waited till they naturally occurred. - When the white-eyed male was crossed with a red-eyed female, all the offspring had red eyes (dominant), when crossing the f1 generation, it produced a classic 3:1 ratio but the white-eyed trait only appeared in males, showing it was linked to sex - Genes located on the same chromosome, linked genes, tend to be inherited together because the chromosome is passed along as a unit - Results of crosses with linked genes deviate
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